xmipp3.protocols.protocol_projmatch.protocol_projmatch module

class xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch(**args)

Bases: pwem.protocols.protocol_3d.ProtRefine3D, pwem.protocols.protocol_3d.ProtClassify3D

3D reconstruction and classification using multireference projection matching

FILENAMENUMBERLENGTH = 6

allCtfGroups()

Iterate over all CTF groups.

allIters()

Iterate over all iterations.

allRefs()

Iterate over all references.

angularProjectLibraryStep(iterN, refN, args, stepParams, **kwargs)

assignImagesToReferencesStep(iterN)

calculateDeviationsStep(it)

Calculate both angles and shifts devitations for all iterations

calculateFscStep(iterN, refN, args, constantToAdd, **kwargs)

cleanVolumeStep(vol1, vol2)

convertInputStep()

Generated the input particles metadata expected by projection matching. And copy the generated file to be used as initial docfile for further iterations.

createIterDirsStep(iterN)

Create the necessary directory for a given iteration.

createOutputStep()

executeCtfGroupsStep(**kwargs)

filterVolumeStep(iterN, refN, constantToAddToFiltration, **kwargs)

getLastIter()

initAngularReferenceFileStep()

itersBoolValues(attributeName, firstValue=False)

Take the string of a given attribute and create a list of booleans that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

itersFloatValues(attributeName, firstValue=-1)

Take the string of a given attribute and create a list of floats that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

itersStringValues(attributeName, firstValue='c1')

Take the string of a given attribute and create a list of strings that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

projectionMatchingStep(iterN, refN, args)

reconstructionStep(iterN, refN, program, method, args, suffix, **kwargs)

storeResolutionStep(resolIterMd, resolIterMaxMd, sampling)

transformMaskStep(program, args, **kwargs)

volumeConvertStep(reconstructedFilteredVolume, maskedFileName)